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Few attorneys better understand the legal dilemmas surrounding the U.S. military prison in Guantánamo Bay, Cuba, than Neal Katyal. In 2006, Katyal led a successful Supreme Court case challenging the legality of the Bush Administration's military tribunals in Guantánamo, a ruling that sounded one of the first death knells for Camp X-Ray. But two years later, difficult questions about how to close Guantánamo continue to vex legal minds ranging from Katyal to the advisers now gathering around President-elect Barack Obama. "This is a huge and difficult problem," says Katyal, who teaches national-security law at Georgetown University. "I don't actually see obvious answers."

Obama has vowed to close Guantánamo and reject the Military Commissions Act, the 2006 law underpinning the ongoing Guantánamo tribunals. But major hurdles stand in the way of doing so, even for a new President with a clear mandate.

First, what do you do with the roughly 255 people currently imprisoned at Guantánamo  a group of whom only 23 have been charged? If Obama wanted to move as swiftly as possible to close Guantánamo, the strongest step he could take as President would be to simply shutter the camp by Executive Order and transfer all of the detainees to prison sites inside the U.S. At that point, in theory, the detainees would face four possible fates: being charged with offenses that could be tried in federal courts; court-marshaled according to the Uniform Code of Military Justice; turned over to the governments of their native countries; or simply released. (See pictures from inside Camp X-Ray at Guantánamo here.)

Many civil rights activists say existing military and civilian criminal courts can handle the Guantánamo cases and decide on the disposition of each of those 255 individuals, despite the Bush Administration's arguments otherwise. But the legal limbo many Guantánamo detainees have endured for years still poses significant problems. That is because the primary purpose of detaining these people was not to stage trials but rather to gain usable intelligence through interrogation. Forming proper criminal cases at this point would be difficult.

Take for example the case of Khalid Sheikh Mohammed, the most senior al-Qaeda operative in U.S. custody. At present, his case and many other prominent ones appear essentially stalled at the specially formed military commissions, which the Obama campaign has pledged to halt. But prosecuting Mohammed and other cases like his in federal court may prove tricky. At least some of the evidence against Mohammed looks to have been gathered during harsh interrogations, which may make it inadmissible in court. His arrest and detention had none of the necessary steps provided under U.S. civilian law that help safeguard the rights of suspects  and sometimes allow for loopholes for some to minimize or evade prosecution. Many of the same legal obstacles would arise in any attempt to court-martial Mohammed, because regular military courts have comparable rules about evidence and legal procedure.

There are, at bottom, no good options for trying Mohammed and the roughly 14 others the government appears intent on prosecuting, because the Bush Administration has held them for so many years by Executive Orders in contravention of regular U.S. criminal and military law. Then there's the question of what to do with future suspected terrorists who are caught in an indefinite war on terrorism if there is no more Guantánamo. Alleged terrorist operatives will continue to fall into the hands of the FBI, CIA and military in the years ahead. Obama may consider working to create so-called national-security courts, which would essentially be a hybrid tribunal system blending military and civilian criminal law. Those who support the creation of national-security courts say that only a new, carefully constructed system can effectively deal with issues like classified evidence and other matters that sometimes snarl proceedings in regular criminal and military courts.

The idea has some prominent backers, including Katyal and former assistant attorney general Jack Goldsmith, who clashed with senior Bush Administration officials over Guantánamo and other issues during his time at the Justice Department. The Associated Press, citing unnamed Obama advisers, reported Monday that the President-elect plans to put forward proposals for a new court to handle some Guantánamo cases. But many legal thinkers disagree with such an approach, arguing that all such cases should be prosecuted in federal courts, which have proven effective in many instances. Also, many argue that new national-security courts would likely face the same difficulties as the ongoing Guantánamo tribunals, which have floundered because of procedural snafus while drawing hundreds of constitutional challenges. "Lots of people are opposed, and for many good reasons," Katyal said of the proposed national-security courts.

The emerging Obama transition team has yet to spell out its plans for closing Guantánamo officially. Campaign officials say the President-elect is still forming the legal team that will advise him on that and other issues once he begins making decisions as President. Obama has not spoken on the issue since winning the presidential election and has offered no signs that he discussed the matter with President Bush when visiting the White House on Monday. But there's little doubt that the Guantánamo problem Bush leaves behind for Obama will be one of the hardest the President-elect will face when he finally sits in the Oval Office.